{"id":"https://openalex.org/W2943903654","doi":"https://doi.org/10.1371/journal.pcbi.1006933","title":"An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis","display_name":"An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis","publication_year":2019,"publication_date":"2019-05-09","ids":{"openalex":"https://openalex.org/W2943903654","doi":"https://doi.org/10.1371/journal.pcbi.1006933","mag":"2943903654","pmid":"https://pubmed.ncbi.nlm.nih.gov/31071076"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006933","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006933","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1006933","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001517455","display_name":"Niki Karagianni","orcid":"https://orcid.org/0000-0002-1240-5684"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Niki Karagianni","raw_affiliation_strings":["Biomedcode Hellas SA, Vari, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedcode Hellas SA, Vari, Greece","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085228735","display_name":"Ksanthi Kranidioti","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ksanthi Kranidioti","raw_affiliation_strings":["Biomedcode Hellas SA, Vari, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedcode Hellas SA, Vari, Greece","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003741192","display_name":"Nikolaos Fikas","orcid":"https://orcid.org/0000-0001-9363-7171"},"institutions":[{"id":"https://openalex.org/I142617266","display_name":"University of Crete","ror":"https://ror.org/00dr28g20","country_code":"GR","type":"education","lineage":["https://openalex.org/I142617266"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Nikolaos Fikas","raw_affiliation_strings":["Department of Biology, University of Crete, Heraklion, Greece"],"raw_orcid":"https://orcid.org/0000-0001-9363-7171","affiliations":[{"raw_affiliation_string":"Department of Biology, University of Crete, Heraklion, Greece","institution_ids":["https://openalex.org/I142617266"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060569015","display_name":"Maria Tsochatzidou","orcid":null},"institutions":[{"id":"https://openalex.org/I142617266","display_name":"University of Crete","ror":"https://ror.org/00dr28g20","country_code":"GR","type":"education","lineage":["https://openalex.org/I142617266"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Maria Tsochatzidou","raw_affiliation_strings":["Department of Biology, University of Crete, Heraklion, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Crete, Heraklion, Greece","institution_ids":["https://openalex.org/I142617266"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023050756","display_name":"Panagiotis Chouvardas","orcid":"https://orcid.org/0000-0003-1527-3151"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]},{"id":"https://openalex.org/I6820528","display_name":"Alexander Fleming Biomedical Sciences Research Center","ror":"https://ror.org/013x0ky90","country_code":"GR","type":"facility","lineage":["https://openalex.org/I6820528"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Panagiotis Chouvardas","raw_affiliation_strings":["Department of Physiology, School of Medicine, National Kapodistrian University, Athens, Greece","Institute of Immunology, Biomedical Sciences Research Center (BSRC), 'Alexander Fleming', Vari, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physiology, School of Medicine, National Kapodistrian University, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Institute of Immunology, Biomedical Sciences Research Center (BSRC), 'Alexander Fleming', Vari, Greece","institution_ids":["https://openalex.org/I6820528"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009922302","display_name":"Maria C. Denis","orcid":"https://orcid.org/0000-0003-3926-9261"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Maria C. Denis","raw_affiliation_strings":["Biomedcode Hellas SA, Vari, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedcode Hellas SA, Vari, Greece","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062268324","display_name":"George Kollias","orcid":"https://orcid.org/0000-0003-1867-3150"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]},{"id":"https://openalex.org/I6820528","display_name":"Alexander Fleming Biomedical Sciences Research Center","ror":"https://ror.org/013x0ky90","country_code":"GR","type":"facility","lineage":["https://openalex.org/I6820528"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"George Kollias","raw_affiliation_strings":["Department of Physiology, School of Medicine, National Kapodistrian University, Athens, Greece","Institute of Immunology, Biomedical Sciences Research Center (BSRC), 'Alexander Fleming', Vari, Greece"],"raw_orcid":"https://orcid.org/0000-0003-1867-3150","affiliations":[{"raw_affiliation_string":"Department of Physiology, School of Medicine, National Kapodistrian University, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]},{"raw_affiliation_string":"Institute of Immunology, Biomedical Sciences Research Center (BSRC), 'Alexander Fleming', Vari, Greece","institution_ids":["https://openalex.org/I6820528"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024197769","display_name":"Christoforos Nikolaou","orcid":null},"institutions":[{"id":"https://openalex.org/I142617266","display_name":"University of Crete","ror":"https://ror.org/00dr28g20","country_code":"GR","type":"education","lineage":["https://openalex.org/I142617266"]},{"id":"https://openalex.org/I4210105723","display_name":"FORTH Institute of Molecular Biology and Biotechnology","ror":"https://ror.org/01gzszr18","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210105723","https://openalex.org/I8901234"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Christoforos Nikolaou","raw_affiliation_strings":["Department of Biology, University of Crete, Heraklion, Greece","Institute of Molecular Biology and Biotechnology (IMBB), Foundation of Research and Technology (FORTH), Heraklion, Greece"],"raw_orcid":"https://orcid.org/0000-0003-3001-6786","affiliations":[{"raw_affiliation_string":"Department of Biology, University of Crete, Heraklion, Greece","institution_ids":["https://openalex.org/I142617266"]},{"raw_affiliation_string":"Institute of Molecular Biology and Biotechnology (IMBB), Foundation of Research and Technology (FORTH), Heraklion, Greece","institution_ids":["https://openalex.org/I4210105723"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5001517455","https://openalex.org/A5024197769"],"corresponding_institution_ids":["https://openalex.org/I142617266","https://openalex.org/I4210105723"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.3179,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.8213637,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"15","issue":"5","first_page":"e1006933","last_page":"e1006933"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11503","display_name":"Cytokine Signaling Pathways and Interactions","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11503","display_name":"Cytokine Signaling Pathways and Interactions","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10200","display_name":"Rheumatoid Arthritis Research and Therapies","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11668","display_name":"interferon and immune responses","score":0.9890000224113464,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.8347171545028687},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.5723965167999268},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.537087619304657},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5245352387428284},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4805043935775757},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4703376889228821},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.44078493118286133},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.4064130485057831},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.29297366738319397},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2571820020675659},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.07470282912254333}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.8347171545028687},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.5723965167999268},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.537087619304657},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5245352387428284},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4805043935775757},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4703376889228821},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.44078493118286133},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.4064130485057831},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.29297366738319397},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2571820020675659},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.07470282912254333}],"mesh":[{"descriptor_ui":"D000068582","descriptor_name":"Certolizumab Pegol","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000068582","descriptor_name":"Certolizumab Pegol","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000068582","descriptor_name":"Certolizumab Pegol","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000068879","descriptor_name":"Adalimumab","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000068879","descriptor_name":"Adalimumab","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000068879","descriptor_name":"Adalimumab","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000069285","descriptor_name":"Infliximab","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000069285","descriptor_name":"Infliximab","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000069285","descriptor_name":"Infliximab","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001168","descriptor_name":"Arthritis","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D001168","descriptor_name":"Arthritis","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D001168","descriptor_name":"Arthritis","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D001168","descriptor_name":"Arthritis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001168","descriptor_name":"Arthritis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001168","descriptor_name":"Arthritis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001172","descriptor_name":"Arthritis, Rheumatoid","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D001172","descriptor_name":"Arthritis, Rheumatoid","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D001172","descriptor_name":"Arthritis, Rheumatoid","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D004195","descriptor_name":"Disease Models, Animal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004195","descriptor_name":"Disease Models, Animal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004195","descriptor_name":"Disease Models, Animal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007249","descriptor_name":"Inflammation","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D007249","descriptor_name":"Inflammation","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D007249","descriptor_name":"Inflammation","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008810","descriptor_name":"Mice, Inbred C57BL","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008810","descriptor_name":"Mice, Inbred C57BL","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008810","descriptor_name":"Mice, Inbred C57BL","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008822","descriptor_name":"Mice, Transgenic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008822","descriptor_name":"Mice, Transgenic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008822","descriptor_name":"Mice, Transgenic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016896","descriptor_name":"Treatment Outcome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016896","descriptor_name":"Treatment Outcome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016896","descriptor_name":"Treatment Outcome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059451","descriptor_name":"Biosimilar Pharmaceuticals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059451","descriptor_name":"Biosimilar Pharmaceuticals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059451","descriptor_name":"Biosimilar Pharmaceuticals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1006933","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006933","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:31071076","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31071076","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1006933","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006933","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:5094f51aae0041c1a3cf06bdc32a9807","is_oa":true,"landing_page_url":"https://doaj.org/article/5094f51aae0041c1a3cf06bdc32a9807","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 15, Iss 5, p e1006933 (2019)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/8101784","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/An_integrative_transcriptome_analysis_framework_for_drug_efficacy_and_similarity_reveals_drug-specific_signatures_of_anti-TNF_treatment_in_a_mouse_model_of_inflammatory_polyarthritis/8101784","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:6508611","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6508611","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006933","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006933","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.6100000143051147}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W132781887","https://openalex.org/W1920379674","https://openalex.org/W1964215887","https://openalex.org/W1973012451","https://openalex.org/W1981094412","https://openalex.org/W1984146900","https://openalex.org/W1987971958","https://openalex.org/W2016381774","https://openalex.org/W2025642864","https://openalex.org/W2029463219","https://openalex.org/W2037882607","https://openalex.org/W2040847667","https://openalex.org/W2045919491","https://openalex.org/W2048075876","https://openalex.org/W2049220563","https://openalex.org/W2054655013","https://openalex.org/W2058688253","https://openalex.org/W2072633203","https://openalex.org/W2078550582","https://openalex.org/W2080902390","https://openalex.org/W2100382163","https://openalex.org/W2102746921","https://openalex.org/W2105422073","https://openalex.org/W2114768841","https://openalex.org/W2119544631","https://openalex.org/W2124954099","https://openalex.org/W2141314333","https://openalex.org/W2142122490","https://openalex.org/W2147031534","https://openalex.org/W2148668599","https://openalex.org/W2160341576","https://openalex.org/W2410978489","https://openalex.org/W2463343942","https://openalex.org/W2473562090","https://openalex.org/W2597501795","https://openalex.org/W2606291386","https://openalex.org/W2608527598","https://openalex.org/W2624392734","https://openalex.org/W2765964749","https://openalex.org/W2788255482","https://openalex.org/W2791033272","https://openalex.org/W2805310212","https://openalex.org/W2860509233","https://openalex.org/W2911964244","https://openalex.org/W2943547636","https://openalex.org/W2952615074","https://openalex.org/W4210547217"],"related_works":["https://openalex.org/W1976510917","https://openalex.org/W3155641129","https://openalex.org/W2073305407","https://openalex.org/W2052655934","https://openalex.org/W104645380","https://openalex.org/W2027213253","https://openalex.org/W2017047508","https://openalex.org/W2165201120","https://openalex.org/W2023641020","https://openalex.org/W2188530857"],"abstract_inverted_index":{"Anti-TNF":[0],"agents":[1],"have":[2,233],"been":[3,42],"in":[4,29,111,128,161,192,209,236,243],"the":[5,63,117,120,129,182,229,253,277,282,287,290],"first":[6],"line":[7],"of":[8,10,24,34,50,55,62,69,77,83,95,103,131,175,199,228,239,255,279,284,289,292],"treatment":[9,61,104],"various":[11],"inflammatory":[12,71,220],"diseases":[13],"such":[14],"as":[15],"Rheumatoid":[16],"Arthritis":[17],"and":[18,89,119,146,219,261,268,271,286],"Crohn's":[19],"Disease,":[20],"with":[21],"a":[22,47,75,162,173,226,273],"number":[23,174],"different":[25,57,132],"biologics":[26,59,133,208],"being":[27],"currently":[28],"use.":[30],"A":[31],"detailed":[32,97],"analysis":[33,49,88],"their":[35,210],"effect":[36],"at":[37,185],"transcriptome":[38],"level":[39],"has":[40],"nevertheless":[41],"lacking.":[43],"We":[44,73,202],"herein":[45],"present":[46],"concise":[48],"an":[51,186],"extended":[52],"transcriptomics":[53],"profiling":[54],"four":[56],"anti-TNF":[58,207],"upon":[60],"established":[64],"hTNFTg":[65],"(Tg197)":[66],"mouse":[67],"model":[68],"spontaneous":[70],"polyarthritis.":[72],"implement":[74],"series":[76],"computational":[78],"analyses":[79,257],"that":[80,106,138,177],"include":[81],"clustering":[82],"differentially":[84],"expressed":[85],"genes,":[86],"functional":[87,144],"random":[90],"forest":[91],"classification.":[92],"Taking":[93],"advantage":[94],"our":[96],"sample":[98],"structure,":[99],"we":[100,224],"devise":[101],"metrics":[102],"efficiency":[105,211],"take":[107],"into":[108],"account":[109],"changes":[110],"gene":[112,136,264],"expression":[113,137,197],"compared":[114],"to":[115,134,142,149,158,181,194,212,217,232,246,258],"both":[116],"healthy":[118,196],"diseased":[121],"state.":[122],"Our":[123,250],"results":[124],"suggest":[125],"considerable":[126],"variability":[127],"capacity":[130,193],"modulate":[135,213],"can":[139],"be":[140],"attributed":[141],"treatment-specific":[143,263],"pathways":[145,244],"differential":[147],"preferences":[148],"restore":[150,195],"over-":[151],"or":[152],"under-expressed":[153,200,240],"genes.":[154,201],"Early":[155],"intervention":[156],"appears":[157],"manage":[159],"inflammation":[160],"more":[163],"efficient":[164],"way":[165],"but":[166],"is":[167,189],"accompanied":[168],"by":[169],"increased":[170],"effects":[171],"on":[172],"genes":[176,215,241,270],"are":[178],"seemingly":[179],"unrelated":[180,269],"disease.":[183],"Administration":[184],"early":[187],"stage":[188],"also":[190],"lacking":[191],"levels":[198],"record":[203],"quantifiable":[204],"differences":[205],"among":[206],"over-expressed":[214],"related":[216,245],"immune":[218],"pathways.":[221],"More":[222],"importantly,":[223],"find":[225],"subset":[227],"tested":[230],"substances":[231],"quantitative":[234],"advantages":[235],"addressing":[237],"deregulation":[238],"involved":[242],"known":[247],"RA":[248],"comorbidities.":[249],"study":[251],"shows":[252],"potential":[254],"transcriptomic":[256],"identify":[259],"comprehensive":[260],"distinct":[262],"signatures":[265],"combining":[266],"disease-related":[267],"proposes":[272],"generalized":[274],"framework":[275],"for":[276],"assessment":[278],"drug":[280],"efficacy,":[281],"search":[283],"biosimilars":[285],"evaluation":[288],"efficacy":[291],"TNF":[293],"small":[294],"molecule":[295],"inhibitors.":[296]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
